Most genes are regulated by a complex array of interactions, resulting in unique gene expression patterns. Such gene expression patterns vary between different cell types, cells at different developmental stages or differentiation states, and cells exposed to signaling molecules, stress, infection, or other cellular condition or disorder. Efforts to understand the processes that regulate variant gene expression patterns have concentrated on early events in transcription regulation and in events surrounding translation. In contrast, much less attention has been paid to the role of mRNA-protein complexes (mRNP complexes) in post-transcriptional regulatory processes, such as the regulation of stability, localization, and translation efficiency of mRNAs. Still less is known about the post-transcriptional processes that coordinate the expression of functionally related genes (e.g., genes that share or participate in a certain function or pathway), which are often co-localized to particular mRNP complexes and bound to the same RNA binding protein (RBP).
Post-transcriptional gene regulation of some mRNAs is mediated by regulatory elements or sequences that reside in both the introns and exons of pre-mRNAs, and the coding and noncoding regions of mature transcripts. One example of such a regulatory element is the AU-rich instability element (ARE) present in the 3′-untranslated regions (UTRs) of early-response gene mRNAs, many of which encode proteins essential for growth and differentiation. RNA binding proteins associated with mRNP complexes bind to AREs in vitro and mediate post-transcriptional mRNA stability and translation in vivo. However, not all mRNAs that bind to an RNA binding protein possess an ARE or other common regulatory element. Moreover, the mechanism(s) by which an RNA binding protein recognizes mRNAs that do not contain an ARE is not known.
In vitro binding assays using RNA binding proteins have shown that the mRNAs that are associated with a particular RNA binding protein are often structurally or functionally related. However, these in vitro methods do not reflect the dynamic nature of mRNA association with MRNP complexes in vivo, which changes in response to intra- and inter-cellular signaling events. A need therefore exists for reliable methods for monitoring RNA binding protein-mRNA interactions, as well as the association of mRNAs and proteins with mRNP complexes in vivo. The use of such methods will allow for the characterization of mRNA-protein interactions and their functional implications, will elucidate biological pathways, and will further allow for the identification of therapeutic targets and therapeutics.